EVOLBIOLAB: Bacterial Evolution

• The Earth is approximately 4.5 billion years old.
• The first evidence for microbial life can be found in rocks around 3.86 billion years old.
• Assignment of names for species and higher groups of prokaryotes is regulated by the International Code of Nomenclature of Bacteria.
• Classification is the organization of organisms into progressively more inclusive groups on the basis of either phenotypic similarity or evolutionary relationship.
• Prokaryotes are given descriptive genus names and species epithets following the binomial system of nomenclature used throughout biology.
• Carl Woese pioneered the use of SSU rRNA for phylogenetic studies in the 1970s, establishing the presence of three domains of life: Bacteria, Archaea, and Eukarya.
• As lineages diverged, distinct metabolisms developed.
• O2 could not accumulate until it reacted with abundant reduced materials in the oceans such as FeS and FeS2.
• Comparative rRNA sequencing is a routine procedure that involves the amplification of the gene encoding SSU rRNA, sequencing of the amplified gene, and analysis of sequence in reference to other sequences.
• Development of oxygenic photosynthesis dramatically changed the course of evolution.
• Other genetic changes include gene duplication, horizontal gene transfer, and gene loss.
• Molecular evidence suggests that the ancestors of Bacteria and Archaea diverged about 4 billion years ago.
• Mutations are changes in the nucleotide sequence of an organism’s genome, occurring because of errors in replication, UV radiation, and other factors.
• Formation of the ozone layer provides a barrier against UV radiation, allowing life to continue on the surface of the Earth.
• Cytoplasmic membrane contains S0 reductase.
• Banded iron formations are laminated sedimentary rocks; a prominent feature in the geological record.
• Cyanobacteria developed a photosystem that could use H2O instead of H2S, generating O2.
• Alternative source of H2 in the cytoplasm is provided by primitive hydrogenase and primitive ATPase.
• By 2.4 billion years ago, O2 concentrations raised to 1 part per million, initiating the Great Oxidation Event.
• Endosymbiosis is a well-supported hypothesis for the origin of eukaryotic cells, contending that mitochondria and chloroplasts arose from symbiotic association of prokaryotes within another type of cell.
• Phylogeny is the evolutionary history of a group of organisms, inferred from nucleotide sequence data.
• The Ribosomal Database Project (RDP) is a large collection of rRNA sequences, currently containing over 409,000 sequences.
• Adaptative mutations improve the fitness of an organism, increasing its survival.
• Bacteria, Archaea, and Eukarya are the three domains of life.
• Major assumptions of the molecular clock approach are that nucleotide changes occur at a constant rate, are generally neutral, and are random.
• The 16S gene is an ancestral cell marker and can be used to align sequences and generate a tree.
• The 16S gene can be amplified by PCR.
• Domain Eukaryota consists of two major groups: Crenarchaeota and Euryarchaeota.
• Phenotypic analysis examines the morphological, metabolic, physiological, and chemical characters of the cell.
• DNA can be isolated from the cell.
• Prokaryotes, Eukaryotes, LUCA, Flavobacteria, Thermotoga, Thermodesulfobacterium, Aquifex, Cyanobacteria, Chloroplast, Proteobacteria, Mitochondrion, and Gram-positive bacteria are examples of bacterial phyla.
• Bacterial taxonomy incorporates multiple methods for identification and description of new species, including the polyphasic approach.
• Green nonsulfur bacteria, Crenarchaeota, Euryarchaeota, Thermoproteus, Pyrodictium, Thermococcus, Marine Crenarchaeota, Methano-bacterium, Methano-coccus, Pyrolobus, Methanosarcina, Thermoplasma, Methanopyrus, Extreme halophiles, Entamoebae, Slime molds, Animals, Fungi, Plants, Ciliates, Flagellates, Trichomonads, Microsporidia, Diplomonads, and Giardia are examples of Archaea and Eukarya phyla.
• Sequences can be run on agarose gel to check for correct size.
• GC ratio is a method of genotypic analysis that compares G+C content of DNA from different organisms.
• Domain Bacteria contains at least 80 major evolutionary groups (phyla) and many groups are defined from environmental sequences alone.
• Genotypic analysis includes DNA–DNA hybridization, DNA profiling, Multilocus sequence typing (MLST), and GC ratio.
• Kilo- bases are represented as 1, 2, 3, 4, 5, 3.0–, 2.0–, 1.5–, 1.0–, 0.5–.
• Multilocus sequence typing (MLST) is a method in which several different “housekeeping genes” from an organism are sequenced.
• DNA–DNA hybridization involves hybridizing genomes of two organisms to examine proportion of similarities in their gene sequences.